How to execute custom Python code on startup?
Go to File -> User Preferences and select the "File" tab. In the dialog, there is a "Scripts" entry where you can define the location of an alternative scripts directory.

If you want to deploy this change to a lot of blender installations, simply copy the userpref.blend file to your skeleton/template user home directory. Whenever a new user is created, this file will then be copied to his home directory, and when he starts blender, he'll have the changed script preference. The neat thing is that you can change other preferences values (and the startup blend file, too, if you want) with this. For Linux, the file lives under ~/.config/blender/blendversion/config/userpref.blend. I'm pretty sure that for Windows there is a similar file that gets stored somewhere in the user's homedir.